Re: [PyMOL] efficiency assigning b-factors
Hi Jordan et al.,
Yes one can use the alter command with a whole selection at once and
it is much faster. I hadn't realized that until Thomas Holder helped fix
my script that appears to do what you were wanting to do:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py
The B-factor data is read in and assigned to a dictionary by the
atom_data_extract function elsewhere in the script (indexed either by
chain and residue number, or by chain and ID) and then it is applied
like this:
b_dict = atom_data_extract(data_file)
quiet = int(quiet) == 1
def b_lookup(chain, resi, name, ID, b):
def _lookup(chain, resi, name, ID):
if resi in b_dict[chain] and isinstance(b_dict[chain][resi], dict):
return b_dict[chain][resi][name][0]
else:
# find data by ID
return b_dict[chain][int(ID)][0]
try:
if not chain in b_dict:
chain = ''
b = _lookup(chain, resi, name, ID)
if not quiet: print '///%s/%s/%s new: %f' % (chain, resi, name, b)
except KeyError:
if not quiet: print '///%s/%s/%s keeping: %f' % (chain, resi, name,
b)
return b
stored.b = b_lookup
cmd.alter(mol, '%s=stored.b(chain, resi, name, ID, %s)' % (prop, prop))
cmd.rebuild()
Hope that helps.
Cheers,
Rob
On Tue, 2015-06-16 11:10 EDT, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Jordan,
The answer is something like (assuming reading from a file):
newb=[float(i) for i in open(stuff.dat).read().split()]
alter n. ca, b=newb.pop()
spectrum b
Hope it helps,
Tsjerk
On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis
jwillis0...@gmail.com wrote:
Hi Tsjerk,
It seems everyone is pointing to this (
http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
which I somehow missed. However, they seem to be altering one
residue at a time like I’m doing.
Jordan
On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Jordan,
Yes, although I don't have the answer at hand, it has been given on
the user list several times. You can find it in the archives.
Cheers,
Tsjerk
On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com
wrote:
Hi,
I have a dictionary that has a bunch of values I want to assign to
b-factors in order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason,
its taking forever in my script. Is there something inherently
inefficient about alter? And is there anyway to fix it? Perhaps,
assign a bunch of b-factors at once.
Jordan
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Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical Molecular Sciences, Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc
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Re: [PyMOL] efficiency assigning b-factors
Hi Jordan -
I think you're doing it exactly the way I would, given an existing dict
containing the values. Note, however, that if you have multiple loaded, or
multiple chains with the same residue numbers, you may wish to be more specific
with your selection string; your current script will alter every residue with
the given resi # in all chains of all loaded objects.
If you're having to do this multiple times with the same structure and it's
slow each time (e.g. while creating a figure from a script), maybe consider
saving a new PDB file with the modified B-factors using PyMOL's `save` command,
so you can just load it directly.
# After your `alter` script
save myfile_mod_b.pdb, myfile
# Then next time load the new version with the same name
# as before to avoid breaking the rest of the script. Now you can
# remove the `alter` for-loop from the script.
load myfile_mod_b.pdb, myfile
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jun 16, 2015, at 2:15 AM, Jordan Willis
jwillis0...@gmail.commailto:jwillis0...@gmail.com wrote:
Hi,
I have a dictionary that has a bunch of values I want to assign to b-factors in
order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason, its taking
forever in my script. Is there something inherently inefficient about alter?
And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.
Jordan
--
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Re: [PyMOL] efficiency assigning b-factors
Hi Jordan,
Yes, although I don't have the answer at hand, it has been given on the
user list several times. You can find it in the archives.
Cheers,
Tsjerk
On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com wrote:
Hi,
I have a dictionary that has a bunch of values I want to assign to
b-factors in order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason, its
taking forever in my script. Is there something inherently inefficient
about alter? And is there anyway to fix it? Perhaps, assign a bunch of
b-factors at once.
Jordan
--
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Re: [PyMOL] efficiency assigning b-factors
Hi Tsjerk,
It seems everyone is pointing to this
(http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring
http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
which I somehow missed. However, they seem to be altering one residue at a time
like I’m doing.
Jordan
On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Jordan,
Yes, although I don't have the answer at hand, it has been given on the user
list several times. You can find it in the archives.
Cheers,
Tsjerk
On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com
mailto:jwillis0...@gmail.com wrote:
Hi,
I have a dictionary that has a bunch of values I want to assign to b-factors
in order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason, its taking
forever in my script. Is there something inherently inefficient about alter?
And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.
Jordan
--
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Re: [PyMOL] efficiency assigning b-factors
Hi Jordan,
The answer is something like (assuming reading from a file):
newb=[float(i) for i in open(stuff.dat).read().split()]
alter n. ca, b=newb.pop()
spectrum b
Hope it helps,
Tsjerk
On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis jwillis0...@gmail.com
wrote:
Hi Tsjerk,
It seems everyone is pointing to this (
http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
which I somehow missed. However, they seem to be altering one residue at a
time like I’m doing.
Jordan
On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Jordan,
Yes, although I don't have the answer at hand, it has been given on the
user list several times. You can find it in the archives.
Cheers,
Tsjerk
On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com wrote:
Hi,
I have a dictionary that has a bunch of values I want to assign to
b-factors in order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason, its
taking forever in my script. Is there something inherently inefficient
about alter? And is there anyway to fix it? Perhaps, assign a bunch of
b-factors at once.
Jordan
--
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